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My biggest issue with markdown involves links. Parentheses are allowed in URLs and those confuse most markdown parsers:

I don't know if this is standard or not but there is a way of dealing with that on reddit.

That'll work fine, just insert a backslash before the character and it'll be treated purely as a character instead of a formatting marker.

escaping makes parsing too complex. i'd rather just be forced to use %29, which is the closing parenthesis URL encoded.

Consecutive blockquotes also tend to break for me, leaving me to write all of them in HTML, which is pretty silly.